Instruments such as tandem mass spectrometry (MS/MS) instruments may be used to detect the presence of particular substances such as trace atmospheric gases that may be present in a gas sample. The gas sample may be obtained in a variety of manners including, for example, by collecting air near an individual or luggage or other articles associated with an individual, by collecting air near or within a vehicle, a cargo container, or a room, by heating a swab passed over an individual, an individual's luggage or other articles, or the surfaces of a vehicle, cargo container or room, or by monitoring the ambient air to detect plumes of substances emitted from nearby or distant sources and transported to the monitoring equipment by the wind or by diffusion. To detect trace atmospheric gases in the sample, the detector/analyzer unit of such instruments may employ ion separation and thus require that the gas sample be ionized. However, different substances are ionized more effectively by different modes of ionization.